Signal-Seeker™: Useful Links

 

General: protein and PTM links

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UniProt:The Universal Protein Resource

The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Provides information about well-established PTMs for any target protein.

 

NCBI: Entrez - Gene

Entrez - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

 

ModPred: predictor of post-translational modification sites in proteins

ModPred is a sequence-based predictor of potential post-translational modification (PTM) sites in proteins. It consists of 34 ensembles of logistic regression models, trained separately on a combined set of 126,036 non-redundant experimentally verified sites for 23 different modifications, obtained from public databases and an ad-hoc literature search.

 

Nature, Post-translational modifications: Latest Research and Reviews

Find the latest high impact articles and reviews from an array of journals about an assortment of PTMs. For the latest research on specific PTMs please see the links below.

 

Cell, Post-translational modifications: Latest Research from Cell journals

Find the latest high impact articles from the Cell family of journals about an assortment of PTMs. For the latest research on specific PTMs please see the links below.

 

CPLM (Compendium of Protein Lysine Modifications)

CPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs).

 

ExPASY: Bioinformatics Resource Portal

ExPASY has an array of protein modification resource tools.

 

PTM Statistics Curator: Automated Curation and Population of PTM Statistics from the Swiss-Prot Knowledgebase

The PTM Statistics Curator is an automated computational method for quantifying the number of each post-translational modification reported experimentally and non-experimentally in the Swiss-Prot Knowledgebase. Non-experimental qualifiers (Potential, Probable, By Similarity) are consistent with those defined in Swiss-Prot.

 

SysPTM: A Systematic Resource for Post-Translational Modification

SysPTM provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools.

 

Acetylation specific links

Nature, Acetylation: Latest Research and Reviews

Find the latest high impact articles and reviews from an array of journals about the protein modification, Acetylation.

 

Cell, Acetylation: Latest Research from Cell journals

Find the latest high impact articles from the Cell family of journals about the protein modification, Acetylation.

 

WERAM: Writers, Erasers, and Readers of Acetylation and Methylation

WERAM 1.0 is a comprehensive Eukaryotic Writers, Erasers and Readers protein of Histone Acetylation and Methylation system Database for 148 eukaryotic species.

 

ASEB: A Web Server for KAT-specific Acetylation Site Prediction

Lysine acetylation is one of the important post-translational modifications of both histone and non-histone proteins. Thousands of acetylated proteins are known. However, few lysine acetylation transferases (KAT) responsible for the acetylation of these proteins have been identified. ASEB developed the Acetylation Set Enrichment-Based (ASEB) method to predict the KAT families responsible for a given protein.

 

LysAcet: Lysine Acetylation Predictor

Reversible acetylation on lysine residues, a crucial post-translational modification (PTM) for both histone and non-histone proteins, governs many central cellular processes. Due to limited data and lack of a clear acetylation consensus sequence, little research has focused on prediction of lysine acetylation sites. Incorporating almost all currently available lysine acetylation information, and using the support vector machine (SVM) method along with coding schema for protein sequence coupling patterns, we propose here a novel lysine acetylation prediction algorithm: LysAcet.

 

Phosphotyrosine specific links

Nature, Phosphorylation: Latest Research and Reviews

Find the latest high impact articles and reviews from an array of journals about the protein modification, Phosphorylation.

 

Cell, Phosphorylation: Latest Research from Cell journals

Find the latest high impact articles from the Cell family of journals about the protein modification, Phosphorylation.

 

PhosphoELM: a database of S/T/Y phosphorylation sites

PhosphoELM is a database of S/T/Y phosphorylation sites.

 

RegPhos: Regulatory Network in Protein Phosphorylation

RegPhos is a resource to explore the protein kinase-substrate phosphorylation networks in human and mouse.

 

NetworKIN: explore cellular phosphorylation networks

NetworKIN is a database that allows for the exploration of cellular phosphorylation networks.

 

GPS 3.0: Computational prediction of phosphorylation sites

GPS 3.0 with novel Peptide Selection and Weight Training methods to improve the prediction performance and robustness. Additionally, more than 6,000 phosphorylation sites were used for training and could predict kinase-specific phosphorylation sites for 464 human PKs in hierarchy.

 

SUMOylation specific links

Nature, SUMOylation: Latest Research and Reviews

Find the latest high impact articles and reviews from an array of journals about the protein modification, SUMOylation.

 

Cell, SUMOylation: Latest Research from Cell journals

Find the latest high impact articles from the Cell family of journals about the protein modification, SUMOylation.

 

GPS-SUMO: Prediction of SUMOylation sites and SUMO-binding motifs

Improved prediction algorithm with added, novel SIMs prediction feature.

 

JASSA v4: Joined Advanced Sumoylation Site and Sim Analyser

Uses a scoring system based on a position frequency matrix derived from the alignment of experimental SUMOylation sites or SUMO-interacting motifs (SIMs).

 

Ubiquitination specific links

Nature, Ubiquitylation: Latest Research and Reviews

Find the latest high impact articles and reviews from an array of journals about the protein modification, Ubiquitylation (Ubiquitination).

 

Cell, Ubiquitination: Latest Research from Cell journals

Find the latest high impact articles from the Cell family of journals about the protein modification, Ubiquitination.

 

hUbiquitome: A database of human ubiquitination sites and cascades

hUbiquitome is a public resource for the retrieval of experimentally verified human ubiquination enzymes and substrates. It is the first comprehensive database of human ubiqutitination pathway proteins and ubiquitin binding-site sequences which is freely available to academia.

 

UbiNet: A web resource for exploring ubiquitination networks

UbiNet is a knowledge-based system that could provide potential E3 ligases for ubiquitinated proteins by the information of protein-protein interactions and substrate site specificities.

 

UbPred: predictor of protein ubiquitination sites

UbPred is a random forest-based predictor of potential ubiquitination sites in proteins. It was trained on a combined set of 266 non-redundant experimentally verified ubiquitination sites available from our experiments and from two large-scale proteomics studies (Hitchcock, et al., 2003; Peng, et al., 2003).

 

ESA-UbiSite: A web server for identification of Ubiquitination Sites

Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. In fact, some sites that undergo ubiquitination have not been identified. In this work, we propose an evolutionary screening algorithm (ESA) to select effective negatives from among non-validated sites and an ESA-based prediction method, ESA-UbiSite, to identify human ubiquitination sites. Experimental results show that ESA-UbiSite with effective negatives achieved 0.92 test accuracy, better than existing prediction methods.